Wiki

Function

Find EDAM ontology terms by has_output relation

Description

edamhasoutput searches the has_output relations of EDAM terms and
returns matching terms. The input is read from the installed EDAM
database. The ontology term output can be written to screen, to file,
or passed to another program. A wide range of standard ontology term
formats may be specified for input and output.

By default all terms are returned. Searches can be limited to one or a few namespaces.

data

(Data entity)

entity

(Biological entity)

format

(Data format)

identifier

(Identifier)

operation

(Bioinformatics operation)

resource

(Data resource)

topic

(Field of bioinformatics study)

*

Advanced (Unprompted) qualifiers

-sensitive

boolean

By default, the query keywords are matched against the EDAM term names (and synonyms) only. This option also matches the keywords against the EDAM term definitions and will therefore (typically) report more matches.

Boolean value Yes/No

No

-subclasses

boolean

Extend the query matches to include all terms which are specialisations (EDAM sub-classes) of the matched type.

Boolean value Yes/No

No

-obsolete

boolean

The default behaviour is to not use or return obsolete terms. This option if set will include all terms.

Boolean value Yes/No

No

Associated qualifiers

"-outfile" associated outobo qualifiers

-odirectory2-odirectory_outfile

string

Output directory

Any string

-oformat2-oformat_outfile

string

Ontology term output format

Any string

General qualifiers

-auto

boolean

Turn off prompts

Boolean value Yes/No

N

-stdout

boolean

Write first file to standard output

Boolean value Yes/No

N

-filter

boolean

Read first file from standard input, write first file to standard output

Boolean value Yes/No

N

-options

boolean

Prompt for standard and additional values

Boolean value Yes/No

N

-debug

boolean

Write debug output to program.dbg

Boolean value Yes/No

N

-verbose

boolean

Report some/full command line options

Boolean value Yes/No

Y

-help

boolean

Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose

Boolean value Yes/No

N

-warning

boolean

Report warnings

Boolean value Yes/No

Y

-error

boolean

Report errors

Boolean value Yes/No

Y

-fatal

boolean

Report fatal errors

Boolean value Yes/No

Y

-die

boolean

Report dying program messages

Boolean value Yes/No

Y

-version

boolean

Report version number and exit

Boolean value Yes/No

N

Input file format

edamhasoutput queries the EDAM ontology.

Output file format

The output is a standard EMBOSS ontology term file.

The results can be output in one of several styles by using the
command-line qualifier -oformat xxx, where 'xxx' is replaced by
the name of the required format. The available format names are: obo,
brief, list, html, xml, json, excel.